Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Bulk RNA Seq Samples

ABSTRACT: We focused on studying the methylation signature of the spectrum of PNSTs to develop a methylome-based classification of these common tumors. We studied the genome-wide DNA methylation patterns using the Illumina MethylationEPIC array and classified the samples into 5 subgroups. Gene Expression comparing the subgroups were performed using bulk RNA Seq

ORGANISM(S): Homo sapiens

PROVIDER: GSE207400 | GEO | 2023/04/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: snRNA Seq Samples

Project description:We focused on studying the methylation signature of the spectrum of PNSTs to develop a methylome-based classification of these common tumors. We studied the genome-wide DNA methylation patterns using the Illumina MethylationEPIC array and classified the samples into 5 subgroups. Gene Expression comparing the subgroups were performed using single nuclear RNA Seq

2023-04-03 | GSE207399 | GEO

Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Methylation Samples

2023-04-03 | GSE207207 | GEO

Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Methylation Samples

Project description:Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Methylation Samples

| PRJNA854154 | ENA

Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: snRNA Seq Samples

Project description:Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: snRNA Seq Samples

| PRJNA855245 | ENA

Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Bulk RNA Seq Samples

Project description:Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Bulk RNA Seq Samples

| PRJNA855244 | ENA

Methylation profiling of malignant peripheral nerve sheath tumour samples

Project description:Methylation profiling of malignant peripheral nerve sheath tumours (MPNSTs), epithelioid MPNSTs, sarcoma NOS, melanomas and spindle cell/sclerosing rhabdomyosarcomas.

2020-07-02 | E-MTAB-8864 | biostudies-arrayexpress

Malignant peripheral nerve sheath tumours in neurofibromatosis 1.

Project description:BackgroundCross sectional studies have shown that 1-2% of patients with neurofibromatosis 1 (NF1) develop malignant peripheral nerve sheath tumours (MPNST). However, no population based longitudinal studies have assessed lifetime risk.MethodsNF1 patients with MPNST were ascertained from two sources for our north west England population of 4.1 million in the 13 year period 1984-1996: the North West Regional NF1 Register and review of notes of patients with MPNST in the North West Regional Cancer Registry.ResultsTwenty-one NF1 patients developed MPNST, equivalent to an annual incidence of 1.6 per 1000 and a lifetime risk of 8-13%. There were 37 patients with sporadic MPNST. The median age at diagnosis of MPNST in NF1 patients was 26 years, compared to 62 years in patients with sporadic MPNST (p<0.001). In Kaplan-Meier analyses, the five year survival from diagnosis was 21% for NF1 patients with MPNST, compared to 42% for sporadic cases of MPNST (p=0.09). One NF1 patient developed two separate MPNST in the radiation field of a previous optic glioma.ConclusionThe lifetime risk of MPNST in NF1 is much higher than previously estimated and warrants careful surveillance and a low threshold for investigation.

| S-EPMC1735122 | biostudies-literature

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

Project description:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. Using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumours (MPNST), benign Neurofibromas and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. Contrary to the current dogma, significant global hypomethylation was not observed in the MPNST methylome. However, a highly significant (P<10-100) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNST. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs). Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLM-NM-1) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P<10-60), non-CGI-associated promoters (P<10-4) and hypomethylated cDMRs in SINE repeats (P<10-100) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyse cancer methylomes. Examination of methylation profiles in malignant, benign and normal tissue

2011-01-01 | E-GEOD-21714 | biostudies-arrayexpress

Proteogenomic landscape of medulloblastoma subgroups [methylation]

Project description:Proteogenomic landscape of medulloblastoma subgroups [methylation]

| PRJNA413673 | ENA

Malignant Peripheral Nerve Sheath Tumors: From Epigenome to Bedside.

Project description:Malignant peripheral nerve sheath tumors (MPNST) are aggressive sarcomas typically developing in the context of neurofibromatosis type 1 (NF-1). With the exception of surgical resection, these tumors are resistant to all current therapies, and unresectable, recurrent, or metastatic tumors are considered incurable. Preclinical studies have identified several novel candidate molecular targets for therapeutic intervention, but, to date, targeted therapies have proven ineffective. Recent studies have identified recurrent mutations in polycomb repressive complex 2 (PRC2) core components, embryonic ectoderm development protein (EED) and suppressor of zeste 12 homolog (SUZ12), in MPNST. These mutations result in global loss of the histone H3 lysine 27 trimethylation epigenetic mark, normally deposited by PRC2, and subsequent gain in acetylation at this residue. This altered chromatin state has been shown to promote MPNST malignancy; however, acetylation at this residue sensitizes MPNSTs to BRD4 and bromodomain and extra-terminal domain inhibition. Interestingly, the catalytic component of PRC2, enhancer of zeste homolog 2 (EZH2), is not mutated in MPNST, hinting that a noncanonical, PRC2-independent function of EZH2 may play a role in this cancer. This review examines the pathobiology of MPNST, the contribution of PRC2 subunits to this process, and the prospects for PRC2-related therapies for this cancer. IMPLICATIONS: Identification of mutations in the PRC2 components EED and SUZ12 in the majority of MPNSTs may imply noncanonical oncogenic activities of the intact component, EZH2, and provide new opportunities for therapeutic intervention.

| S-EPMC6610818 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data